[English] 日本語
Yorodumi
- PDB-1vjf: CRYSTAL STRUCTURE OF A PUTATIVE DNA-BINDING PROTEIN (CC_0111) FRO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vjf
TitleCRYSTAL STRUCTURE OF A PUTATIVE DNA-BINDING PROTEIN (CC_0111) FROM CAULOBACTER CRESCENTUS CB15 AT 1.62 A RESOLUTION
ComponentsDNA-binding protein, putative
KeywordsDNA BINDING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


aminoacyl-tRNA editing activity / DNA binding
Similarity search - Function
Prolyl-tRNA editing protein ProX/PRXD1 / YbaK protein / YbaK/aminoacyl-tRNA synthetase-associated domain / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA-binding protein, putative
Similarity search - Component
Biological speciesCaulobacter crescentus CB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.62 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative DNA-binding protein from Caulobacter crescentus at 1.62 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-binding protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2514
Polymers20,0311
Non-polymers2203
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.891, 50.891, 121.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-343-

HOH

-
Components

#1: Protein DNA-binding protein, putative


Mass: 20031.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus CB15 (bacteria) / Species: Caulobacter vibrioides / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ABV9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 33.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.8
Details: 1.0M sodium citrate, 0.1M Tris pH 7.0, 0.2M NaCl, pH 7.8, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0000, 0.9796, 0.9794
DetectorType: ADSC / Detector: CCD / Date: Oct 1, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97961
30.97941
ReflectionResolution: 1.62→60.72 Å / Num. obs: 20981 / % possible obs: 99.4 % / Redundancy: 7.7 % / Biso Wilson estimate: 25.41 Å2 / Rsym value: 0.059 / Net I/σ(I): 19.3
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 1498 / Rsym value: 0.562 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.2.0000refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.62→46.94 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.609 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.076
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16673 1077 5.1 %RANDOM
Rwork0.14488 ---
obs0.146 19865 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.787 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.62→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 13 172 1455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221350
X-RAY DIFFRACTIONr_bond_other_d0.0010.021282
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9561828
X-RAY DIFFRACTIONr_angle_other_deg0.81932977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3295168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74624.3158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46915236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.666157
X-RAY DIFFRACTIONr_chiral_restr0.0970.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021473
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02261
X-RAY DIFFRACTIONr_nbd_refined0.2180.2240
X-RAY DIFFRACTIONr_nbd_other0.1720.21233
X-RAY DIFFRACTIONr_nbtor_other0.0840.2807
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2118
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.222
X-RAY DIFFRACTIONr_mcbond_it2.3753900
X-RAY DIFFRACTIONr_mcbond_other0.5413344
X-RAY DIFFRACTIONr_mcangle_it2.67851362
X-RAY DIFFRACTIONr_scbond_it4.4318541
X-RAY DIFFRACTIONr_scangle_it5.98911465
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 71 4.75 %
Rwork0.185 1424 -
Refinement TLS params.Method: refined / Origin x: 11.916 Å / Origin y: 9.972 Å / Origin z: 79.249 Å
111213212223313233
T-0.0695 Å20.0211 Å20.0086 Å2--0.0156 Å20.0178 Å2---0.0971 Å2
L1.5754 °2-0.128 °2-0.4375 °2-0.8905 °20.4608 °2--0.9649 °2
S-0.1337 Å °-0.1335 Å °-0.0419 Å °0.0789 Å °0.0699 Å °0.0422 Å °0.1249 Å °0.0921 Å °0.0638 Å °
Refinement TLS groupSelection: ALL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more